If you are running MusE with jack, as I suppose you do, please try starting jack with the extra argument -Xseq to enable the midi bridge to alsa.
Alternatively start MusE with the argument -A to allow MusE to connect directly to alsa-midi.

As for the devicelist you mention, I suppose it is a configuration file with presets and similar?
I'd be happy if you could send it here, or point me to where such can be found. I haven't looked at them but it is probably possible to make a converter to the muse midi-device format.

Not sure what you mean by manually adjusting the MIDI configuration, could you give an example what you need to do that you would want to do only once?

MusE has a template system so you can create a song file with some prepared configuration, e.g. instantiated softsynths, created midi tracks. But I don't think this is what you are asking for.